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Background: In recent years, clustering algorithms have been effectively applied in molecular biology for gene expression data analysis. With the help of clustering algorithms such as K-means, hierarchical clustering, SOM, etc, genes are partitioned into groups based on the similarity between their expression profiles. In this way, functionally related genes are identified. As the amount of laboratory data in molecular biology grows exponentially each year due to advanced technologies such as Microarray, new efficient and effective methods for clustering must be developed to process this growing amount of biological data. Results: In this paper, we propose a new clustering algorithm, Incremental Genetic K-means Algorithm (IGKA). IGKA is an extension to our previously proposed clustering algorithm, the Fast Genetic K-means Algorithm (FGKA). IGKA outperforms FGKA when the mutation probability is small. The main idea of IGKA is to calculate the objective value Total Within-Cluster Variation (TWCV) and to cluster centroids incrementally whenever the mutation probability is small. IGKA inherits the salient feature of FGKA of always converging to the global optimum. C program is freely available at http://database.cs.wayne.edu/proj/FGKA/index.htm. Conclusions: Our experiments indicate that, while the IGKA algorithm has a convergence pattern similar to FGKA, it has a better time performance when the mutation probability decreases to some point. Finally, we used IGKA to cluster a yeast dataset and found that it increased the enrichment of genes of similar function within the cluster.

Hybrid clones segregating human chromosomes were prepared by fusing mouse RAG cells to fresh human bone marrow cells and tested for the mixed-function oxygenase [flavoprotein-linked monooxygenase; RH, reduced-flavoprotein:oxygen oxidoreductase (RH-hydroxylating); EC 1.14.14.1] arylhydrocarbon hydrocarbon hydroxylase. Neither constitutive nor induced aryl hydrocarbon hydroxylase activity was detected in parental RAG cells. Induced aryl hydrocarbon hydroxylase was expressed in 4 out of 12 primary and 12 out of 19 secondary hybrid clones examined. Constitutive hydroxylase activity was detectable in 9 of the 15 inducible clones. All of the hybrid clones that exhibited constitutive hydroxylase activity were also inducible. There was a positive correlation between constitutive and induced hydroxylase activities although the absolute levels of the enzyme showed a wide range between different clones. Isozyme analysis performed on 12 primary and 19 secondary hybrid clones showed that aryl hydrocarbon hydroxylase activity was concordant with the expression of the human isozymes malate dehydrogenase (EC 1.1.1.37) and isocitrate dehydrogenase (EC 1.1.1.42), previously assigned to human chromosome 2. Isozyme markers for 19 other human chromosomes segregated independently from aryl hydrocarbon hydroxylase activity. The results suggest that the gene(s) required for aryl hydrocarbon hydroxylase activity are located on human chromosome 2.

Badawy et al. (1973, 1975, 1979, 198Oa, 198Ob) have shown in many reports that chronic alcohol ingestion by rats results in higher central nervous system (CNS) levels of tryptophan (Trp) and serotonin (WIT). They argue that this occurs because chronic ethanol intake inhibits synthesis of hepatic tryptophan oxygenase (TPO), the major quantitative catabolic enzyme for Trp metabolism (Young et al. 1978). Extrapolating from rats to humans, such a biochemical process suggests that drinking behavior might be reinforced by the higher brain Trp and 5-HT concentrations resulting from ethanol-induced suppression of TPO. Though data on this matter are confusing and inconsistent, it has been shown in the rat that higher brain concen~ations of Trp and 5-HT, resulting from inhibition of hepatic TPO, are associated with altered CNS function (Litman and Correia 1985). Finally, the report that zimelidine reduced drinking behavior among recently detoxified alcoholics (Naranjo et al. 1984) is not only consistent with a role for 5

Although family-planning clinics are numerous and well-accepted in most Australian capital cities, such clinics have been difficult to establish in some Victorian rural towns. One such clinic was established at a rural base hospital in a Victorian town in 1984. The history of the clinic's development and its mode of operation are discussed. The profiles of 157 consecutive new patients who attended the clinic are presented. Comparisons are made with the patient profiles from a Melbourne family-planning clinic. The clinic also provides a separate weekly educational programme. The effect of the educational service in attracting patients to the clinic also was evaluated. Over all, it was concluded that the successful establishment of this clinic has been a result of the appointment of female medical and nursing staff members, the support of the local base hospital, an active media campaign and the development of a separate and concurrent educational programme that was conducted by clinic staff members. It is recommended that these factors be considered in the future development of such clinics in rural areas.

We describe a Drosophila DNA clone of tandemly duplicated genes encoding an amino acid sequence nearly identical to human ribosomal protein S14 and yeast rp59. Despite their remarkably similar exons, the locations and sizes of introns differ radically among the Drosophila, human, and yeast (Saccharomyces cerevisiae) ribosomal protein genes. Transcripts of both Drosophila RPS14 genes were detected in embryonic and adult tissues and are the same length as mammalian S14 message. Drosophila RPS14 was mapped to region 7C5-9 on the X chromosome. This interval also encodes a previously characterized Minute locus, M(1)7C.

Meristematic activity of sterile pea ( Pisum sativum L.) root-tips was abolished within 24 hr after presentation of 10 mM borate to the culture medium. Transfer of borate-repressed root-tips showing no mitotic activity to borate-free medium resulted in resumption of mitosis within 2 hr; control-level mitotic activity and normal distribution of mitotic figures were observed within 6 hr; Analysis of studies with tritiated thymidine labeling suggest that borate arrest of mitosis is during G 2 . Calcium ion reversed the borate repression of mitotic activity.

Our previously described immunoadsorption method for the isolation of vesicles containing the insulin-responsive intracellular glucose transporters from 3T3-L1 adipocytes has been improved in two ways. First, the minimal number of g minutes required to sediment the plasma membranes from the cell homogenate has been determined and, as a result, the supernatant used for immunoadsorption in the new procedure contained twice as much of the intracellular transporters. Second, the immunoadsorption has been performed with affinity-purified antibodies directed against the carboxy terminal peptide of the transporter, rather than against the entire protein. 10 7 cells (10 mg protein) yielded about 12 μg of vesicular protein and 11 μg of vesicular phospholipid. The transporter constituted 3% of the protein in the vesicles; this amount equates to approx. eight copies of the transporter per 50 nm vesicle. The polypeptide composition of the vesicles was determined by gel electrophoresis and protein staining. Major components, other than the glucose transporter, are polypeptides of M r 270 000, 245 000, 165 000 and 115 000. The vesicles contained several phosphoproteins; the major ones have a M r of 245 000, 190 000, 115 000 and 25 000. Insulin treatment of adipocytes did not significantly change the phosphoprotein composition of the vesicles. The vesicles were not enriched in the Golgi marker enzyme, galactosyltransferase. The cellular content of the marker for the trans -Golgi reticulum, sialytransferase, was too low to detect.

Revertants of unc-15(e73)I, a paralyzed mutant with an altered muscle paramyosin, include six dominant and two recessive intragenic unc-15 revertants, two new alleles of the previously identified suppressor gene, sup-3 V, and a new suppressor designated sup-19(m210)V. The recessive intragenic unc-15 revertants exhibit novel alterations in paramyosin paracrystal structure and distribution, and these alterations are modified by interaction with unc-82(e1220)IV, another mutation that affects paramyosin. A strain containing both unc-15 and a mutation in sup-3 V that restores movement was mutagenized, and paralyzed mutants resembling unc-15 were isolated. Twenty mutations that interfere with suppression were divided into three classes (nonmuscle, sus-1, and mutations within sup-3) based on phenotype, genetic map position and dominance. The nonmuscle mutations include dumpy and uncoordinated types that have no obvious direct effect on muscle organization. Two recessive mutations define a new gene, sus-1 III. These mutations modify the unc-15(e73) phenotype to produce a severely paralyzed, dystrophic double mutant that is not suppressed by sup-3. Five semidominant, intragenic sup-3 antisuppressor mutations, one of which occurred spontaneously, restore the wild-type sup-3 phenotype of nonsuppression. However, reversion of these mutants generated no new suppressor alleles of sup-3, suggesting that the sup-3 antisuppressor alleles are not wild type but may be null alleles.

Near-ultraviolet and visible radiations increased the duration of the mitotic cycle in excised pea root meristems primarily by lengthening the duration of the pre-DNA synthetic period (G1). All radiations tested shortened the duration of the post-DNA synthetic period (G2). The most pronounced effects were exhibited by green radiation, which lengthened the duration of the cell cycle, G1, DNA synthesis (S), and mitosis (M), and shortened the duration of G2. Progression of cells arrested by starvation in G, and G2 into DNA synthesis and mitosis was also affected by light treatments. Green radiation appeared to arrest a group of cells in DNA synthesis as well as in G, and G2. Meristems receiving green and near-ultraviolet radiations exhibited the most rapid progression of G, cells through S and G,.

The Asian citrus psyllid, Diaphorina citri, is an insect vector that transmits Candidatus Liberibacter asiaticus, the causal agent of the Huanglongbing (HLB), or citrus greening disease. This disease has devastated Florida’s citrus industry, and threatens California’s industry as well as other citrus producing regions around the world. To find novel solutions to the disease, a better understanding of the vector is needed. The D. citri genome has been used to identify and characterize genes involved in Wnt signaling pathways. Wnt signaling is utilized for many important biological processes in metazoans, such as patterning and tissue generation. Curation based on RNA sequencing data and sequence homology confirms 24 Wnt signaling genes within the D. citri genome, including homologs for beta-catenin, Frizzled receptors, and seven Wnt-ligands. Through phylogenetic analysis, we classify D. citri Wnt ligands as Wg/Wnt1, Wnt5, Wnt6, Wnt7, Wnt10, Wnt11, and WntA. The D. citri version 3.0 genome with chromosomal length scaffolds reveals a conserved Wnt1-Wnt6-Wnt10 gene cluster with a gene configuration like that in Drosophila melanogaster. These findings provide greater insight into the evolutionary history of D. citri and Wnt signaling in this important hemipteran vector. Manual annotation was essential for identifying high quality gene models. These gene models can be used to develop molecular systems, such as CRISPR and RNAi, which target and control psyllid populations to manage the spread of HLB. Manual annotation of Wnt signaling pathways was done as part of a collaborative community annotation project.

Insects have a segmented body plan that is established during embryogenesis when the anterior–posterior (A–P) axis is divided into repeated units by a cascade of gene expression. The cascade is initiated by protein gradients created by translation of maternally provided mRNAs, localized at the anterior and posterior poles of the embryo. Combinations of these proteins activate specific gap genes to divide the embryo into distinct regions along the anterior–posterior axis. Gap genes then activate pair-rule genes, which are usually expressed in parts of every other segment. The pair-rule genes, in turn, activate expression of segment polarity genes in a portion of each segment. The segmentation genes are generally conserved among insects, although there is considerable variation in how they are deployed. We annotated 25 segmentation gene homologs in the Asian citrus psyllid, Diaphorina citri. Most of the genes expected to be present in D. citri based on their phylogenetic distribution in other insects were identified and annotated. Two exceptions were eagle and invected, which are present in at least some hemipterans, but were not found in D. citri. Many of the segmentation pathway genes are likely to be essential for D. citri development, and thus they may be useful targets for gene-based pest control methods.

Huanglongbing (HLB), also known as citrus greening disease, is caused by the bacterium Candidatus Liberibacter asiaticus (CLas). It is a serious threat to global citrus production. This bacterium is transmitted by the Asian citrus psyllid, Diaphorina citri (Hemiptera). There are no effective in planta treatments for CLas. Therefore, one strategy is to manage the psyllid population. Manual annotation of the D. citri genome can identify and characterize gene families that could be novel targets for psyllid control. The yellow gene family is an excellent target because yellow genes, which have roles in melanization, are linked to development and immunity. Combined analysis of the genome with RNA-seq datasets, sequence homology, and phylogenetic trees were used to identify and annotate nine yellow genes in the D. citri genome. Manual curation of genes in D. citri provided in-depth analysis of the yellow family among hemipteran insects and provides new targets for molecular control of this psyllid pest. Manual annotation was done as part of a collaborative Citrus Greening community annotation project.

Chitin deacetylases (CDAs) are one of the least understood components of insect chitin metabolism. The partial deacetylation of chitin polymers appears to be important for the proper formation of higher order chitin structures, such as long fibers and bundles, which contribute to the integrity of the insect exoskeleton and other structures. Some CDAs may also be involved in bacterial defense. Here, we report the manual annotation of four CDA genes from the Asian citrus psyllid, Diaphorina citri, laying the groundwork for future study of these genes.

The polysaccharide chitin is critical for the formation of many insect structures, including the exoskeleton, and is required for normal development. Here we report the annotation of three genes from the chitin synthesis pathway in the Asian citrus psyllid, Diaphorina citri (Hemiptera: Liviidae), the vector of Huanglongbing (citrus greening disease). Most insects have two chitin synthase (CHS) genes but, like other hemipterans, D. citri has only one. In contrast, D. citri is unusual among insects in having two UDP-N-acetylglucosamine pyrophosphorylase (UAP) genes. One of the D. citri UAP genes is broadly expressed, while the other is expressed predominantly in males. Our work helps pave the way for potential utilization of these genes as pest control targets to reduce the spread of Huanglongbing.

As a sensory response to starvation or overcrowding, Caenorhabditis elegans second-stage larvae may molt into a developmentally arrested state called the dauer larva. When environmental conditions become favorable for growth, dauer larvae mold and resume development. Some mutants unable to form dauer larvae are simultaneously affected in a number of sensory functions, including chemotaxis and mating. The behavior and sensory neuroanatomy of three such mutants, representing three distinct genetic loci, have been determined and compared with wild-type strain. Morphological abnormalities in afferent nerve endings were detected in each mutant. Both amphid and outer labial sensilla are affected in the mutant CB1377 (daf-6)X, while another mutant, CB1387 (daf-10)IV, is abnormal in amphidial cells and in the tips of the cephalic neurons. The most pleitropic mutant, CB1379 (che-3)I, exhibits gross abnormalities in the tips of virtually all anterior and posterior sensory neurons. The primary structural defect in CB1377 appears to be in the nonneuronal amphidial sheath cells. The disruption of neural organization in CB1377 is much greater in the adult than in the L2 stage. Of all the anterior sense organs examined, only the amphids are morphologically affected in all three mutants. Thus, one or more of the amphidial neurons may mediate the sensory signals for entry into the dauer larva stage in normal animals. Using temperature-sensitive mutants we determined that the same defects which block entry into the dauer stage also prevent recovery of dauer larvae.

Hybrid cells were formed from mouse RAG cells and fresh human bone marrow cells. The expression of the mixed-function oxidase, aryl hydrocarbon hydroxylase (AHH), in 15 out of 31 hybrid clones correlated with the presence of the human isozymes malate dehydrogenase and isocitrate dehydrogenase, known markers for chromosome 2. AHH activity was not detectable in the parental mouse cell line. Isozyme markers for 17 other chromosomes segregated independently of AHH activity in the mouse x human cell hybrids. The results suggest that the structural gene(s) for AHH are located on human chromosome 2.

Synaptosomes, i.e. functional nerve terminals, were first prepared from mammalian tissue by Gray and Whittaker (1962). Their ease of preparation (reviewed by Jones, 1975), and their metabolic competence, has led to their widespread use in the study of synaptic transmission. One major disadvantage of the synaptosome preparation is its heterogeneity, a consequence of the highly complex nature of the mammalian central nervous system. In order to study the molecular basis of transmission in cholinergic neurones, other non-mammalian systems have been used - in particular the purely cholinergic nerves which innervate the electric organ of Torpedo fish. Synaptosomes prepared from this source (Israel et al, 1976; Dowdall and Zimmermann, 1977) are homogeneous with respect to transmitter type, but there are still problems in extrapolating some data from Torpedo to mammalian systems; especially as it is now becoming apparent that there is heterogeneity in cholinergic nerve terminals derived from differing mammalian brain regions (Richardson et al, 1987).

Rat adrenal S-adenosymethione (SAM) levels and phenylethanolamin-N-methltransferase (PNMT) activity were measured under conditions of hypophysectomy and stress. A new dual-label radioenzymatic assay for SAM is presented which eliminates problems found to exist with previous methods. Strain-specific differences in both PNMT and SAM were found, as well as sex differences in SAM levels. Immobilization stress resulted in an increase in adrenal SAM and PNMT activity, while hypophysectomy decreased both. The distribution of SAM between cortex and medulla did not change with either hypophysectomy or stress. Hypophysectomized Fisher rats were found to be capable of increasing PNMT activity in the absence of increased SAM levels.

One of the most important inhibitory modulators of synaptic transmission in mammalian brain is adenosine. At some cholinergic terminals, adenosine is known to inhibit further release of acetyl-choline. It is unclear whether adenosine is released directly at the synapse or whether ATP is co-released with transmitter and hydro-lysed to adenosine in the synaptic cleft1–4. Methods used in the past for isolating nerve terminals have not yielded homogeneous preparations, making it impossible to determine whether sufficient ATP or adenosine is released at specific synapses for inhibition of transmitter release to occur. Immunoaffinity purification techniques5–8 have recently permitted the preparation of homogeneous populations of cholinergic nerve terminals9, which release ATP upon stimulation10. We now report that in immunoisolated cholinergic nerve terminals from the striatum synaptic ectophos-phohydrolases convert this ATP to adenosine, which inhibits further acetylcholine release, but this inhibitory effect is not seen in cortical cholinergic terminals lacking the complete ectophospho-hydrolase pathway. Therefore the differing adenosine-mediated modulation in different brain areas is controlled by the presence and activity of synaptic ectophosphohydrolases.

Mycoplasmas were examined on the surfaces of tissue culture cells prepared for transmission and scanning electron microscopy. The pleomorphic bodies seen were proved to be mycoplasmas by the use of thin sections, passage of the infection from one cell line to another, and by autoradiography with [ 3 H]thymidine both on the sections and the replicas. The mycoplasmas were not always evenly distributed over the cell's surface; their arrangement seemed to correlate with the activity or morphology of the cell. The use of replicas and scanning electron microscopy in routine examination of cultures for mycoplasma contamination is discussed.

Cholinergic nerve terminals were affinity purified from rat caudate nucleus. On stimulation with both 22.6 mM KCl and 50 microM veratridine, ATP was released in a Ca2+-dependent manner. The molar ratio of released acetylcholine to ATP (9:1) was closer to that found in isolated cholinergic vesicles (7:1) than whole terminals (3:1). Extracellular [14C]ATP was rapidly metabolized by these terminals to adenosine and inosine via ectonucleotidases. The terminals had a saturable, high-affinity uptake mechanism for adenosine (Km = 16.6 microM). Veratridine stimulation also caused the Ca2+-dependent release of nucleosides in a dipyridamole-sensitive manner. Both theophylline treatment and inhibition of extracellular ATP breakdown resulted in increased ATP and nucleoside release. Extracellular adenosine was shown to inhibit acetylcholine release, probably via the A1 receptor. The role of extracellular purines at the cholinergic nerve terminal is discussed.

Rhizobium trifolii 0403 was treated with 16.6 mM succinate and other nutrients and thereby induced to grow in nitrogen-free medium. The organism grew microaerophilically on either semisolid or liquid medium, fixing atmospheric nitrogen to meet metabolic needs. Nitrogen fixation was measured via 15 N incorporation (18% 15 N enrichment in 1.5 doublings) and acetylene reduction. Nitrogen-fixing cells had a K m for acetylene of 0.07 atm (ca. 7.09 kPa), required about 3% oxygen for optimum growth in liquid medium, and showed a maximal specific activity of 5 nmol of acetylene reduced per min per mg of protein at 0.04 atm (ca. 4.05 kPa) of acetylene. The doubling time on N-free liquid medium ranged from 1 to 5 days, depending on oxygen tension, with an optimum temperature for growth of about 30°C. Nodulation of white clover by the cultures showing in vitro nitrogenase activity indicates that at least part of the population maintained identity with wild-type strain 0403.

Background Differential expression (DE) analysis of RNA-seq data still poses inferential challenges, such as handling of transcripts characterized by low expression levels. In this study, we use a plasmode-based approach to assess the relative performance of alternative inferential strategies on RNA-seq transcripts, with special emphasis on transcripts characterized by a small number of read counts, so-called low-count transcripts, as motivated by an ecological application in prairie grasses. Big bluestem (Andropogon gerardii) is a wide-ranging dominant prairie grass of ecological and agricultural importance to the US Midwest while edaphic subspecies sand bluestem (A. gerardii ssp. Hallii) grows exclusively on sand dunes. Relative to big bluestem, sand bluestem exhibits qualitative phenotypic divergence consistent with enhanced drought tolerance, plausibly associated with transcripts of low expression levels. Our dataset consists of RNA-seq read counts for 25,582 transcripts (60 % of which are classified as low-count) collected from leaf tissue of individual plants of big bluestem (n = 4) and sand bluestem (n = 4). Focused on low-count transcripts, we compare alternative ad-hoc data filtering techniques commonly used in RNA-seq pipelines and assess the inferential performance of recently developed statistical methods for DE analysis, namely DESeq2 and edgeR robust. These methods attempt to overcome the inherently noisy behavior of low-count transcripts by either shrinkage or differential weighting of observations, respectively. Results Both DE methods seemed to properly control family-wise type 1 error on low-count transcripts, whereas edgeR robust showed greater power and DESeq2 showed greater precision and accuracy. However, specification of the degree of freedom parameter under edgeR robust had a non-trivial impact on inference and should be handled carefully. When properly specified, both DE methods showed overall promising inferential performance on low-count transcripts, suggesting that ad-hoc data filtering steps at arbitrary expression thresholds may be unnecessary. A note of caution is in order regarding the approximate nature of DE tests under both methods. Conclusions Practical recommendations for DE inference are provided when low-count RNA-seq transcripts are of interest, as is the case in the comparison of subspecies of bluestem grasses. Insights from this study may also be relevant to other applications focused on transcripts of low expression levels. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2442-7) contains supplementary material, which is available to authorized users.